Merge branch 'release-2.2.x'

.editorconfig

@@ -0,0 +1,32 @@
+
+# Special property that should be specified
+# at the top of the file outside of any sections.
+# Set to true to stop .editorconfig files search
+# on current file.
+root = true
+
+[*] #All type of file
+end_of_line = lf
+charset = utf-8
+trim_trailing_whitespace = true
+insert_final_newline = true
+
+[*.js]
+indent_style = space
+tab_width = 4
+
+[*.yml]
+indent_style = space
+indent_size = 2
+
+[package.json]
+indent_style = space
+indent_size = 2
+
+[*.md]
+trim_trailing_whitespace = false
+
+[*.{html,js,md}]
+block_comment_start = /**
+block_comment = *
+block_comment_end = */

.eslintrc.json

@@ -1,5 +1,12 @@
 {
-  "extends": ["eslint:recommended", "google", "plugin:cypress/recommended"],
+  "root":true,
+  "extends": [
+    "eslint:recommended",
+    "google",
+    "plugin:cypress/recommended",
+    "plugin:wc/recommended",
+    "plugin:lit/recommended"
+  ],
   "parser": "babel-eslint",
   "parserOptions": {
     "ecmaVersion": 6,
@@ -11,7 +18,7 @@
   },
   "rules": {
     "indent": ["error", 4, { "SwitchCase": 1, "ignoredNodes": ["TemplateLiteral *"] }],
-    "max-len": ["error", 200],
+    "max-len": ["error", 230],
     "no-console": ["error", { "allow": ["log", "warn", "error", "time", "timeEnd"] }],
     "no-param-reassign": ["warn", { "props": true }],
     "no-undef": ["warn"],
@@ -20,7 +27,7 @@
     "no-use-before-define": ["error", { "classes": false }],
     "padded-blocks": ["error", { "classes": "always" }],
     "quotes": ["warn", "double"],
-    "comma-dangle": ["error", "never"],
+    "comma-dangle": ["error", "only-multiline"],
     "arrow-parens": ["error","as-needed"],
     "no-invalid-this": 0,
     "babel/no-invalid-this": 0,
@@ -38,6 +45,20 @@
     "one-var":  ["error", { "initialized": "never", "uninitialized": "always" }]
   },
   "plugins": [
-    "cypress"
-  ]
+    "cypress",
+    "lit"
+  ],
+  "overrides": [
+    {
+      "files": ["*.js"],
+      "rules": {
+        "lit/no-property-change-update": 0,
+        "cypress/no-unnecessary-waiting": 0
+      }
+    }
+  ],
+  "globals": {
+    "$": true,
+    "globalThis": true
+  }
 }

.github/workflows/build-jsorolla-workflow.yml

@@ -0,0 +1,47 @@
+name: "Reusable workflow to build JSorolla"
+
+on:
+  workflow_call:
+    outputs:
+      version:
+        description: "JSorolla version"
+        value: ${{ jobs.build-jsorolla-workflow.outputs.version }}
+
+jobs:
+  build-jsorolla-workflow:
+    name: Build JSorolla
+    runs-on: ubuntu-20.04
+    outputs:
+      version: ${{ steps.package.outputs.version }}
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-node@v2
+        with:
+          node-version: "16"
+      - uses: actions/cache@v2
+        env:
+          cache-name: cache-node-modules
+        with:
+          # npm cache files are stored in `~/.npm` on Linux/macOS
+          path: ~/.npm
+          key: ${{ runner.os }}-build-${{ env.cache-name }}-${{ hashFiles('**/package-lock.json') }}
+          restore-keys: |
+            ${{ runner.os }}-build-${{ env.cache-name }}-
+            ${{ runner.os }}-build-
+            ${{ runner.os }}-
+      - run: npm install
+      - run: npm run build
+      - id: package
+        uses: tyankatsu0105/read-package-version-actions@v1
+      - uses: actions/upload-artifact@v2
+        with:
+          name: jsorolla-build
+          path: build
+          retention-days: 1
+      - uses: actions/upload-artifact@v2
+        with:
+          name: jsorolla-release
+          # TODO: we should rename the iva-VERSION.tar.gz file as jsorolla-VERSION.tar.gz
+          path: iva-${{ steps.package.outputs.version }}.tar.gz
+          retention-days: 1
+

.github/workflows/deploy-jsorolla-workflow.yml

@@ -0,0 +1,33 @@
+name: "Reusable workflow to deploy JSorolla application"
+
+on:
+  workflow_call:
+    inputs:
+      version:
+        type: string
+        required: true
+    secrets:
+      SSH_SWDEV_IP:
+        required: true
+      SSH_SWDEV_USER:
+        required: true
+      SSH_SWDEV_PASSWORD:
+        required: true
+
+jobs:
+  deploy-jsorolla-workflow:
+    name: Deploy JSorolla Application
+    runs-on: ubuntu-20.04
+    steps:
+      - uses: actions/download-artifact@v2
+        with:
+          name: jsorolla-build
+          path: build
+      - uses: garygrossgarten/github-action-scp@release
+        with:
+          local: build
+          remote: /mnt/data/WEB-APPS/dev/jsorolla-${{ inputs.version }}
+          rmRemote: true
+          host: ${{ secrets.SSH_SWDEV_IP }}
+          username: ${{ secrets.SSH_SWDEV_USER }}
+          password: ${{ secrets.SSH_SWDEV_PASSWORD }}

.github/workflows/develop.yml

@@ -0,0 +1,42 @@
+name: "Main Workflow for JSorolla"
+
+on:
+  push:
+    branches:
+      - "develop"
+      - "release-*"
+
+jobs:
+  build:
+    uses: opencb/jsorolla/.github/workflows/build-jsorolla-workflow.yml@develop
+
+  docker:
+    needs: build
+    uses: opencb/jsorolla/.github/workflows/docker-jsorolla-workflow.yml@develop
+    secrets:
+      DOCKER_HUB_USER: ${{ secrets.DOCKER_HUB_USER }}
+      DOCKER_HUB_PASSWORD: ${{ secrets.DOCKER_HUB_PASSWORD }}
+
+  deploy:
+    needs: build
+    uses: opencb/jsorolla/.github/workflows/deploy-jsorolla-workflow.yml@develop
+    with:
+      version: ${{ needs.build.outputs.version }}
+    secrets:
+      SSH_SWDEV_IP: ${{ secrets.SSH_SWDEV_IP }}
+      SSH_SWDEV_USER: ${{ secrets.SSH_SWDEV_USER }}
+      SSH_SWDEV_PASSWORD: ${{ secrets.SSH_SWDEV_PASSWORD }}
+
+#  notify:
+#    name: Notify private repository
+#    runs-on: ubuntu-20.04
+#    needs: build
+#    steps:
+#      - uses: actions/checkout@v2
+#      - name: Invoke workflow in a private repo
+#        uses: benc-uk/workflow-dispatch@v1
+#        with:
+#          workflow: Docker publish
+#          ref: ${{ github.event.push.head.ref }}
+#          repo: ${{ secrets.JSOROLLA_PRIVATE_REPO }}
+#          token: ${{ secrets.ZG_PERSONAL_TOKEN }}

.github/workflows/docker-jsorolla-workflow.yml

@@ -0,0 +1,26 @@
+name: "Reusable workflow to publish JSorolla in DockerHub"
+
+on:
+  workflow_call:
+    secrets:
+      DOCKER_HUB_USER:
+        required: true
+      DOCKER_HUB_PASSWORD:
+        required: true
+
+jobs:
+  docker-jsorolla-workflow:
+    name: Publish JSorolla Docker
+    runs-on: ubuntu-20.04
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/download-artifact@v2
+        with:
+          name: jsorolla-build
+          path: build
+      - uses: docker/login-action@v1
+        with:
+          username: ${{ secrets.DOCKER_HUB_USER }}
+          password: ${{ secrets.DOCKER_HUB_PASSWORD }}
+      - run: python3 ./docker/docker-build.py push --images app
+

.github/workflows/release.yml

@@ -0,0 +1,34 @@
+name: "Release"
+
+on:
+  push:
+    tags:
+      - "*"
+
+jobs:
+  build:
+    uses: opencb/jsorolla/.github/workflows/build-jsorolla-workflow.yml@develop
+
+  docker:
+    needs: build
+    uses: opencb/jsorolla/.github/workflows/docker-jsorolla-workflow.yml@develop
+    secrets:
+      DOCKER_HUB_USER: ${{ secrets.DOCKER_HUB_USER }}
+      DOCKER_HUB_PASSWORD: ${{ secrets.DOCKER_HUB_PASSWORD }}
+
+  release:
+    needs: [build, docker]
+    uses: opencb/java-common-libs/.github/workflows/release-github-workflow.yml@develop
+    with:
+      artifact: jsorolla-release
+      file: iva-${{ needs.build.outputs.version }}.tar.gz
+
+  deploy:
+    needs: build
+    uses: opencb/jsorolla/.github/workflows/deploy-jsorolla-workflow.yml@develop
+    with:
+      version: ${{ needs.build.outputs.version }}
+    secrets:
+      SSH_SWDEV_IP: ${{ secrets.SSH_SWDEV_IP }}
+      SSH_SWDEV_USER: ${{ secrets.SSH_SWDEV_USER }}
+      SSH_SWDEV_PASSWORD: ${{ secrets.SSH_SWDEV_PASSWORD }}

.gitignore

@@ -1,10 +1,15 @@
 
 build/
+build-next/
 dist/
 *node_modules/
 *web_modules/
 bower_components/
 grunt/
+dist-genome/
+custom-conf
+custom-sites
+*.tar.gz
 
 npm-debug.log
 
@@ -44,3 +49,10 @@ local.properties
 # PDT-specific
 .buildpath
 
+# Cypress
+fixtures
+screenshots
+support
+videos
+mochawesome-report
+

.husky/.gitignore

@@ -0,0 +1 @@
+_

.husky/pre-commit

@@ -0,0 +1,5 @@
+#!/bin/sh
+. "$(dirname "$0")/_/husky.sh"
+
+npm run lint:js
+# npm test